--- /dev/null
+package fr.orsay.lri.varna.models.annotations;
+
+import java.awt.Color;
+import java.awt.Shape;
+import java.awt.geom.GeneralPath;
+import java.awt.geom.Point2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.LinkedList;
+
+import javax.xml.transform.sax.TransformerHandler;
+
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.AttributesImpl;
+
+import fr.orsay.lri.varna.VARNAPanel;
+import fr.orsay.lri.varna.controlers.ControleurClicMovement;
+import fr.orsay.lri.varna.models.VARNAConfigLoader;
+import fr.orsay.lri.varna.models.rna.ModeleBase;
+import fr.orsay.lri.varna.models.rna.RNA;
+import fr.orsay.lri.varna.models.rna.VARNAPoint;
+import fr.orsay.lri.varna.utils.XMLUtils;
+import fr.orsay.lri.varna.views.VueHighlightRegionEdit;
+import fr.orsay.lri.varna.views.VueUI;
+
+public class HighlightRegionAnnotation implements Serializable {
+
+ public static final String HEADER_TEXT = "HighlightRegionAnnotation";
+
+ private static final long serialVersionUID = 7087014168028684775L;
+ public static final Color DEFAULT_OUTLINE_COLOR = Color.decode("#6ed86e");
+ public static final Color DEFAULT_FILL_COLOR = Color.decode("#bcffdd");
+ public static final double DEFAULT_RADIUS = 16.0;
+
+ private Color _outlineColor = DEFAULT_OUTLINE_COLOR;
+ private Color _fillColor = DEFAULT_FILL_COLOR;
+ private double _radius = DEFAULT_RADIUS;
+ private ArrayList<ModeleBase> _bases;
+
+ public static String XML_ELEMENT_NAME = "region";
+ public static String XML_VAR_OUTLINE_NAME = "outline";
+ public static String XML_VAR_FILL_NAME = "fill";
+ public static String XML_VAR_RADIUS_NAME = "radius";
+
+ public void toXML(TransformerHandler hd) throws SAXException
+ {
+ AttributesImpl atts = new AttributesImpl();
+ atts.addAttribute("","",XML_VAR_OUTLINE_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_outlineColor));
+ atts.addAttribute("","",XML_VAR_FILL_NAME,"CDATA",""+XMLUtils.toHTMLNotation(_fillColor));
+ atts.addAttribute("","",XML_VAR_RADIUS_NAME,"CDATA",""+_radius);
+ hd.startElement("","",XML_ELEMENT_NAME,atts);
+ XMLUtils.toXML(hd, _bases);
+ hd.endElement("","",XML_ELEMENT_NAME);
+ }
+
+ public HighlightRegionAnnotation(RNA r, int startIndex, int stopIndex)
+ {
+ this(r.getBasesBetween(startIndex, stopIndex));
+ }
+
+ public HighlightRegionAnnotation()
+ {
+ this(new ArrayList<ModeleBase>());
+ }
+
+ public HighlightRegionAnnotation(ArrayList<ModeleBase> b)
+ {
+ this(b,DEFAULT_FILL_COLOR,DEFAULT_OUTLINE_COLOR,DEFAULT_RADIUS);
+ }
+
+
+ public HighlightRegionAnnotation(ArrayList<ModeleBase> b,Color fill, Color outline, double radius)
+ {
+ _bases = b;
+ _fillColor = fill;
+ _outlineColor = outline;
+ _radius = radius;
+ }
+
+ public HighlightRegionAnnotation clone()
+ {
+ return new HighlightRegionAnnotation(_bases,_fillColor,_outlineColor,_radius);
+ }
+
+ public int getMinIndex()
+ {
+ int min = Integer.MAX_VALUE;
+ for (ModeleBase mb : _bases)
+ {
+ min = Math.min(min, mb.getIndex());
+ }
+ return min;
+ }
+
+ public int getMaxIndex()
+ {
+ int max = Integer.MIN_VALUE;
+ for (ModeleBase mb : _bases)
+ {
+ max = Math.max(max, mb.getIndex());
+ }
+ return max;
+ }
+
+
+ public void setOutlineColor(Color c)
+ {
+ _outlineColor = c;
+ }
+
+ public ArrayList<ModeleBase> getBases()
+ {
+ return _bases;
+ }
+
+ public void setBases(ArrayList<ModeleBase> b)
+ {
+ _bases = b;
+ }
+
+ public void setFillColor(Color c)
+ {
+ _fillColor = c;
+ }
+
+ public Color getFillColor()
+ {
+ return _fillColor;
+ }
+
+ public Color getOutlineColor()
+ {
+ return _outlineColor;
+ }
+
+ public double getRadius()
+ {
+ return _radius;
+ }
+
+ public void setRadius(double v)
+ {
+ _radius = v;
+ }
+
+ public static final int NUM_STEPS_ROUNDED_CORNERS = 16;
+
+ private Point2D.Double symImage(Point2D.Double p, Point2D.Double center)
+ {
+ return new Point2D.Double(2.*center.x-p.x, 2.*center.y-p.y);
+ }
+
+ private LinkedList<Point2D.Double> buildRoundedCorner(Point2D.Double p1, Point2D.Double p2, Point2D.Double anotherPoint)
+ {
+ LinkedList<Point2D.Double> result = new LinkedList<Point2D.Double>();
+ Point2D.Double m = new Point2D.Double((p1.x+p2.x)/2.0,(p1.y+p2.y)/2.0);
+ double rad = p1.distance(p2)/2.;
+ double angle = Math.atan2(p1.y-m.y, p1.x-m.x);
+
+ double incr = Math.PI/((double)NUM_STEPS_ROUNDED_CORNERS+1);
+
+ Point2D.Double pdir = new Point2D.Double(m.x+rad*Math.cos(angle+Math.PI/2.),m.y+rad*Math.sin(angle+Math.PI/2.));
+ if (pdir.distance(anotherPoint)<p1.distance(anotherPoint))
+ { incr = -incr; }
+
+ for(int k=1;k<=NUM_STEPS_ROUNDED_CORNERS;k++)
+ {
+ double angle2 = angle+k*incr;
+ Point2D.Double interForward = new Point2D.Double(m.x+rad*Math.cos(angle2),m.y+rad*Math.sin(angle2));
+ result.addLast(interForward);
+ }
+ return result;
+ }
+
+
+ public GeneralPath getShape(Point2D.Double[] realCoords,Point2D.Double[] realCenters, double scaleFactor)
+ {
+ GeneralPath p = new GeneralPath();
+ LinkedList<Point2D.Double> pointList = new LinkedList<Point2D.Double>();
+ for (int i = 0;i<getBases().size();i++)
+ {
+ int j1 = getBases().get(i).getIndex();
+ {
+ int j0 = j1-1;
+ int j2 = j1+1;
+ Point2D.Double p0 = new Point2D.Double(0., 0.);
+ Point2D.Double p1 = new Point2D.Double(0., 0.);
+ Point2D.Double p2 = new Point2D.Double(0., 0.);
+ if (i==0)
+ {
+ // Single point
+ if (i==getBases().size()-1)
+ {
+ p1 = realCoords[j1];
+ p0 = new Point2D.Double(p1.x+scaleFactor *getRadius(), p1.y);
+ p2 = new Point2D.Double(p1.x-scaleFactor *getRadius(), p1.y);
+ }
+ else
+ {
+ p1 = realCoords[j1];
+ p2 = realCoords[j2];
+ p0 = symImage(p2, p1);
+ }
+ }
+ else if (i==getBases().size()-1)
+ {
+ p0 = realCoords[j0];
+ p1 = realCoords[j1];
+ p2 = symImage(p0, p1);;
+ }
+ else
+ {
+ p0 = realCoords[j0];
+ p1 = realCoords[j1];
+ p2 = realCoords[j2];
+ }
+
+ double dist1 = p2.distance(p1);
+ Point2D.Double v1 = new Point2D.Double((p2.x-p1.x)/dist1,(p2.y-p1.y)/dist1);
+ Point2D.Double vn1 = new Point2D.Double(v1.y,-v1.x);
+ double dist2 = p1.distance(p0);
+ Point2D.Double v2 = new Point2D.Double((p1.x-p0.x)/dist2,(p1.y-p0.y)/dist2);
+ Point2D.Double vn2 = new Point2D.Double(v2.y,-v2.x);
+ double h = (new Point2D.Double(vn2.x-vn1.x,vn2.y-vn1.y).distance(new Point2D.Double(0,0))/2.0);
+ Point2D.Double vn = new Point2D.Double((vn1.x+vn2.x)/2.0,(vn1.y+vn2.y)/2.0);
+ double D = vn.distance(new Point2D.Double(0.0,0.0));
+ vn.x/= D;
+ vn.y/= D;
+ double nnorm = (D+h*h/D);
+
+ double nnormF = nnorm;
+ double nnormB = nnorm;
+
+
+ Point2D.Double interForward = new Point2D.Double(p1.x + nnormF*scaleFactor *getRadius()*vn.x,
+ p1.y + nnormF*scaleFactor *getRadius()*vn.y);
+ Point2D.Double interBackward = new Point2D.Double(p1.x - nnormB*scaleFactor *getRadius()*vn.x,
+ p1.y - nnormB*scaleFactor *getRadius()*vn.y);
+
+
+ if (pointList.size()>0)
+ {
+ Point2D.Double prev1 = pointList.getLast();
+ Point2D.Double prev2 = pointList.getFirst();
+
+ if ((interForward.distance(prev1)+interBackward.distance(prev2))<(interForward.distance(prev2)+interBackward.distance(prev1)))
+ {
+ pointList.addLast(interForward);
+ pointList.addFirst(interBackward);
+ }
+ else
+ {
+ pointList.addFirst(interForward);
+ pointList.addLast(interBackward);
+ }
+ }
+ else
+ {
+ pointList.addLast(interForward);
+ pointList.addFirst(interBackward);
+ }
+ }
+ }
+ if (getBases().size()==1)
+ {
+ int midl = pointList.size()/2;
+ Point2D.Double mid = pointList.get(midl);
+ Point2D.Double apoint = new Point2D.Double(mid.x+1.,mid.y);
+ LinkedList<Point2D.Double> pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint);
+ pointList.addAll(midl, pointListStart);
+ mid = pointList.get(midl);
+ apoint = new Point2D.Double(mid.x+1.,mid.y);
+ LinkedList<Point2D.Double> pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint);
+ pointList.addAll(0,pointListEnd);
+ }
+ else if (getBases().size()>1)
+ {
+ int midl = pointList.size()/2;
+ Point2D.Double apoint = symImage(pointList.get(midl),pointList.get(midl-1));
+ LinkedList<Point2D.Double> pointListStart = buildRoundedCorner(pointList.get(midl-1), pointList.get(midl), apoint);
+ pointList.addAll(midl, pointListStart);
+ apoint = symImage(realCoords[getBases().get(getBases().size()-1).getIndex()],
+ realCoords[getBases().get(getBases().size()-2).getIndex()]);
+ LinkedList<Point2D.Double> pointListEnd = buildRoundedCorner(pointList.get(pointList.size()-1),pointList.get(0), apoint);
+ pointList.addAll(0,pointListEnd);
+ }
+
+
+ if (pointList.size()>0)
+ {
+ Point2D.Double point = pointList.get(0);
+ p.moveTo((float)point.x, (float)point.y);
+
+ for (int i=1;i<pointList.size();i++)
+ {
+ point = pointList.get(i);
+ p.lineTo((float)point.x, (float)point.y);
+ }
+ p.closePath();
+ }
+ return p;
+ }
+
+
+ public static HighlightRegionAnnotation parseHighlightRegionAnnotation(String txt, VARNAPanel vp)
+ {
+ try
+ {
+ String[] parts = txt.split(":");
+ String[] coords = parts[0].split("-");
+ int from = Integer.parseInt(coords[0]);
+ int to = Integer.parseInt(coords[1]);
+ int i = vp.getRNA().getIndexFromBaseNumber(from);
+ int j = vp.getRNA().getIndexFromBaseNumber(to);
+ Color fill = HighlightRegionAnnotation.DEFAULT_FILL_COLOR;
+ Color outline = HighlightRegionAnnotation.DEFAULT_OUTLINE_COLOR;
+ double radius = HighlightRegionAnnotation.DEFAULT_RADIUS;
+ ArrayList<ModeleBase> bases = vp.getRNA().getBasesBetween(i, j);
+ if (parts.length>1)
+ {
+ try
+ {
+ String[] options = parts[1].split(",");
+ for (int k = 0; k < options.length; k++)
+ {
+ //System.out.println(options[k]);
+ try
+ {
+ String[] data = options[k].split("=");
+ String lhs = data[0].toLowerCase();
+ String rhs = data[1];
+ if (lhs.equals("fill"))
+ {
+ fill = VARNAConfigLoader.getSafeColor(rhs, fill);
+ }
+ else if (lhs.equals("outline"))
+ {
+ outline = VARNAConfigLoader.getSafeColor(rhs, outline);
+ }
+ else if (lhs.equals("radius"))
+ {
+ radius = Double.parseDouble(rhs);
+ }
+ }
+ catch(Exception e)
+ {
+ }
+ }
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ return new HighlightRegionAnnotation(bases,fill,outline,radius);
+ }
+ catch(Exception e)
+ {
+ e.printStackTrace();
+ }
+ return null;
+ }
+
+ public String toString()
+ {
+ //String result = "HighlightRegionAnnotation[";
+ //result += "fill:"+_fillColor.toString();
+ //result += ",outline:"+_outlineColor.toString();
+ //result += ",radius:"+_radius;
+ //return result+"]";
+ String result = "Highlighted region "+getMinIndex()+"-"+getMaxIndex();
+ return result;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff